Origin IGS: tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catacttccttcttgcaaaatattcacagcgttgttcatccttataatctgtatcttcttaagtaaataaattctgctgcaaaggtacagggggatacaggtcgtcacaatagacaaacaacggtgataatagcacta Mask Tandem Repeat Region ================================================ tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Find is-nt database================================================ Query_seq: PI0394:PI0395|PI0394:PI0395:transcriptional regulator, AraC family:Na+-driven multidrug efflux pump:->->:360390..360527 138 tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0394:PI0395|PI0394:PI0395:transcriptional regulator, AraC family:Na+-driven multidrug efflux pump:->->:360390..360527 138 tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0394:PI0395|PI0394:PI0395:transcriptional regulator, AraC family:Na+-driven multidrug efflux pump:->->:360390..360527 138 tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 22 End: 138 ..................... M S I V T T C I P L Y L C S R I Y L L K K I Q I I R M N N A V N I L Q E G S M tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0394:PI0395|PI0394:PI0395:transcriptional regulator, AraC family:Na+-driven multidrug efflux pump:->->:360390..360527 138 tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: pint_PI0394_PI0395|transcriptional regulator, AraC family:Na+-driven multidrug efflux pump|POSITIVE:POSITIVE|[360390,360527]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg tagtgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Inter-species Hit: Count: 1 Min: 4 Max: 138 Len: 135 Subject: NC_002950_PG1446_PG1447|MATE efflux family protein:transcriptional regulator, AraC family|NEGATIVE:NEGATIVE|[1531318,1531452]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:4 Query End:138 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 135 ...tgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg ...tgctattatcaccgttgtttgtctattgtgacgacctgtatccccctgtacctttgcagcagaatttatttacttaagaagatacagattataaggatgaacaacgctgtgaatattttgcaagaaggaagtatg Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUAUUAUCACCGUUGUUUGUCUAUUGUGACGACCUGUAUCCCCCUGUACCUUUGCAGCAGAAUUUAUUUACUUAAGAAGAUACAGAUUAUAAGGAUGAACAACGCUGUGAAUAUUUUGCAAGAAGGAAGUAUG (((...(((((((((((((..(((.((((((....(((((((...(((((....))))).....((((......))))..))))))).)))))))))..)))))))..))).)))....)))............. (-32.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUACUUCCUUCUUGCAAAAUAUUCACAGCGUUGUUCAUCCUUAUAAUCUGUAUCUUCUUAAGUAAAUAAAUUCUGCUGCAAAGGUACAGGGGGAUACAGGUCGUCACAAUAGACAAACAACGGUGAUAAUAGCA .............(((.......((((..(((((((.(((((.....((((((((((....((((.........))))...))))))))))))))).......(((......))).))))))))))).....))) (-29.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 60 11 77 28 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 294 63 23 61 15 pint:PI1390|5end_hypothetical_protein_1311154..1311384_POSITIVE 291 57 13 130 75 pint:PI2154|5end_leucyl-tRNA_synthetase_2099861..2100091_POSITIVE 287 43 5 49 8 pint:PI0749|5end_hypothetical_protein_677234..677464_POSITIVE 286 57 11 219 171 pint:PI1950|5end_iron-regulated_membrane_permease_1904468..1904698_POSITIVE 286 60 14 75 27 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 282 60 14 220 169 pint:PI2064|5end_conserved_hypothetical_protein;_possible_type_I_restriction-modification_system,_S_subunit_2025076..2025306_POSITIVE 276 57 11 214 159 pint:PI0209|5end_hypothetical_protein_202723..202953_POSITIVE 275 66 28 133 90 pint:PI1185|5end_hypothetical_protein_1106076..1106306_POSITIVE 274 61 23 71 35 pint:PI0633|5end_possible_preprotein_translocase,_YajC_subunit_579671..579901_POSITIVE 270 60 11 79 29 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 269 57 13 101 59 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 269 62 23 166 131 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 268 58 13 61 19 pint:PI1619|5end_two-component_system_response_regulator_1543210..1543440_POSITIVE 267 57 12 115 54 pint:PI0330|5end_hypothetical_protein_310447..310677_POSITIVE 266 48 11 46 5 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 266 58 13 128 78 pint:PI0179|5end_hypothetical_protein_171757..171987_POSITIVE 265 51 11 53 1 pint:PI2097|5end_conserved_hypothetical_protein_2050912..2051142_POSITIVE 263 60 11 80 29 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 262 65 24 206 162 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 60 11 68 19 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 326 57 11 149 88 pint:PI1390|3end_hypothetical_protein_1311329..1311479_POSITIVE 275 66 28 140 97 pint:PI1184|3end_conserved_hypothetical_protein_1106163..1106313_POSITIVE 274 61 23 51 15 pint:PI0632|3end_NusB_family_protein_(N_utilization_substance_protein_B)_579731..579881_POSITIVE 269 64 35 70 41 pint:PI0227|3end_ABC_transporter,_ATP-binding/permease_protein_225632..225782_POSITIVE 267 57 12 102 41 pint:PI0329|3end_hypothetical_protein_310514..310664_POSITIVE 266 48 11 110 69 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 265 47 1 149 101 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 261 60 20 115 81 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 260 57 11 137 94 pint:PI1513|3end_conserved_hypothetical_protein_1432502..1432652_POSITIVE 258 63 25 61 27 pint:PI0335|3end_hypothetical_protein_314420..314570_POSITIVE 257 129 81 81 27 pint:PI0275|3end_hypothetical_protein_264489..264639_POSITIVE 254 69 21 92 39 pint:PI0278|3end_hypothetical_protein_265625..265775_POSITIVE 249 58 16 51 9 pint:PI0886|3end_hypothetical_protein_817809..817959_POSITIVE 249 58 12 142 85 pint:PI0460|3end_50S_ribosomal_protein_L3_433132..433282_POSITIVE 248 61 23 126 95 pint:PI0519|3end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_478809..478959_POSITIVE 247 75 46 147 114 pint:PI1575|3end_LemA_protein_1501852..1502002_POSITIVE 244 48 3 150 108 pint:PI1979|3end_conserved_hypothetical_protein_1937327..1937477_POSITIVE 244 47 1 88 21 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 244 72 49 134 111 pint:PI0423|3end_hypothetical_protein_388432..388582_POSITIVE